In 1937, Japan invades China, beginning the Second Sino-Japanese War. The Japanese Imperial Army overruns China’s capital city, Nanking, in December and carries out the systematic and brutal Nanking massacre.
As the invading Japanese overpower the Chinese army, desperate schoolgirls flee to the nominally protective walls of their convent at a Western-run Roman Catholic cathedral. Here, John Miller (Bale), an American mortician on a task to bury the head priest, joins the group of innocent schoolgirls. He finds a boy there, George, an orphan who was raised by the dead priest, and taught English. The boy is the same age as the schoolgirls. Soon a group of flamboyant prostitutes arrive at the cathedral, seeking refuge by hiding in the cellar. Pretending to be a priest, Miller tries to keep everyone safe while trying to repair the convent’s truck to use for an escape.
After an incident when rogue Japanese forces assault the cathedral (who are then killed by the dying effort of a lone Chinese Major (Tong)), Japanese Colonel Hasegawa promises to protect the convent by placing guards outside the gate, and requests that the schoolgirls sing a chorale for him. Several days later, he hands Miller an official invitation for the schoolgirls to sing at the Japanese Army’s victory celebration. Fearing for the safety of the virginal schoolgirls, Miller declines. Hasegawa informs him that it is an order and that the girls are going to be picked up the next day. Before they leave, the Japanese soldiers count the schoolgirls and erroneously include one of the prostitutes (who has strayed from the cellar), totalling 13.
When the de facto leader of the schoolgirls, Shu Juan (Zhang Xinyi), convinces them that they are better off committing suicide by jumping off the cathedral tower, they are saved at the last moment when the de facto leader of the prostitutes, Yu Mo (Ni), convinces her group to protect the schoolgirls by taking their place at the Japanese party. As there are only 12 prostitutes, George, the dead priest’s adoptive son, volunteers as well. Miller initially opposes their self-sacrificing decision, but ultimately assists in disguising them, using his skills as a mortician to adjust their makeup and cut their hair to appear like schoolgirls. The prostitutes also create knives out of broken windows and hide them in their cloaks.
The next day, the “13 Flowers of Nanking” are led away by the unsuspecting Japanese soldiers. After they depart, Miller hides the schoolgirls on the truck he repaired and, using a single-person permit provided by the father of a schoolgirl, drives out of Nanking. In the last scene, the truck is seen driving on a deserted highway heading west, away from the advancing Japanese army. The fate of the 13 Flowers remains unknown, apparently martyring themselves for the students’ freedom.